This is a property of all filters. There is no manufacturing process that produces pores of absolutely uniform size. Â This is why the EPA standards are 99.9999% and not 100% filtration of bacteria. Your best bet is to only buy filters or other treatments which meet this standard.
Don’t let this freak you out. Ingesting a few bacteria or Protozoa rarely leads to illness in immune competent adults. The minimal infectious dose (the amount required to infect 50% of healthy adults) is thought  to be around 10 for giardia cysts and 100 for enteric bacteria that cause diarrheal disease. Those numbers are also averages around a distribution but you get the idea. It would take a fairly epic filter fail in heavily contaminated water to make you sick. Most of the time, anyway.
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